Refactor retrieval graph expansion and enhance scoring logic

[Aaryanverma]

• Updated _expand_graph to incorporate query relevance in scoring, ensuring that nodes are scored based on both proximity and content relevance.
• Improved handling of already expanded nodes to prevent redundant processing and ensure the best score is retained across multiple paths.
• Added tests for the new scoring logic to validate that distant but relevant neighbors are not suppressed and that shared neighbors receive the maximum score regardless of visit order.
• Introduced a new llms.txt file for documentation on the Gray Box system, detailing installation, operational behavior, and configuration.
• Refactored various test files to streamline imports and improve clarity, including tests for interactive input handling, curation, history tracking, and storage.